Quentin Wheeler is a well-known insect systematist interested in biodiversity discovery, phylogenetics, and species concepts. He is University Vice President and Dean of the College of Liberal Arts and Sciences at Arizona State University. He was also one of the founders of the International Institute for Species Exploration at ASU (http://species.asu.edu/index), producers of the great You Tube video "Planet Bob" (http://www.planetbob.asu.edu/index.html), which uses humor to focus attention on biodiversity and taxonomy (and won a 2008 Webby Award).

Schedule and venue:5:30 - social gathering with beverages and informal pizza dinner: cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg., UC Berkeley campus.7:00 - talk followed by discussion, in same room.

Well, I have decided that I need to look beyond just new omic words to snark about here (I have been giving a "Worst New Omics Word Award" every once in a while"). So I am now going to post, as often as I can, a little ditty about any bad omics word that is out there. Yesterday's winner was "phenogenomics" which I posted only to twitter.

Incidentally, 'connectomics' is a cheesy mouthful of a word. Some words just weren't meant to be biologized with the -omics suffix, and 'connect' is one of them. 'Genomics,' cool. 'Proteomics,' a little annoying and not very creative. 'Connectomics,' stop the bus I want to get off. At the very least let's reserve the -omics for molecular biology. Thank goodness Bialek didn't try to pull us into the world of 'infomics.

Tuesday, January 26, 2010

I am writing because I am working on a project to evaluate the importance of finishing microbial genomes. I know there has been lots of talk about this out there on the web and in papers, etc but I think a fresh discussion is useful. To get people up to speed below is a summary of the issue as I see it.

Shotgun sequencing: Genome sequencing relies generally on the shotgun method at the beginning of a project where DNA fragments from an organism of interest are sequenced in a highly random manner.

Assembly: After shotgun sequencing, the genome is assembled as best as possible into larger pieces (called contigs) and ordered sets of contigs (called scaffolds). All of this put together can be called an "assembly"

Gaps: After the assembly phase, there are almost always gaps in the assembly. These generally come in two forms:

sequencing gaps (where we know two contigs go together in some orientation but where we do not know the sequence of the DNA in between the contigs)

physical gaps (where we have sets of scaffolds but do not know how the connect to each other).

Quality: After the assembly phase, different components of the assembly can have different "qualities" where from example, some sections are somewhat ambiguous and others are highly reliable

Finishing: Using any combination of laboratory, computational and other analyses one can both fill in gaps in the assembly and improve the quality of the assembly. This can generally be called "finishing"

Quality of final product: Depending on the end quality of the assembly we could assign it to one of a few categories of "completeness" as outlined in a paper by Patrick Chain et al. In essence, you can consider the post to be a follow up to their paper and their work.

We plan to try to measure what one gains by the finishing steps. We need to know this because we would like to make intelligent decisions about how to allocate resources. If one gains a lot from finishing then it would make sense to allocate significant resources to it. I note, I and some colleagues wrote a paper about this issue "The value of complete microbial genome sequencing (You get what you pay for)" that was published in 2002. This is without a doubt not the only discussion of the topic but I just wanted to point out I have been involved in this debate before. Despite that, I think we simply do not know right now what the benefits might be in the new sequencing landscape.

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So the question I am asking here is:

What do people think are the potential benefits that could come from finishing?

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Here are some possible answers to get the discussion going:

Gene discovery (e.g., there may be interesting/important genes in missing/low quality data)

Esthetics of completeness (as in, it just feels better to have a finished genome)

Also - I note there has been some discussion of this for animals, plants etc (e.g., see recent paper by Eric Green and others on vertebrates) Many of the issues are similar but they are different enough that I think a microbe focused discussion is useful.

The gene products required for the initial invasive predatory processes have not been extensively studied but the genome sequencing of B. bacteriovorus HD100 [1] revealed a genome of 3.85Mb, including a core genome similar to that of non-predatory bacteria and some 40% of the genome comprising a potential predicted “predatosome” of genes, encoding both hydrolytic products that may be employed in prey degradation, and genes that may be required specifically for host predation and thus are not conserved across the Proteobacteria.

The paper is actually quite interesting. They use genomic approaches to characterize a fascinating organism - the bacterial species Bdellovibrio bacteriovorus. This bug is a predatory organism - eating other bacteria. Since it eats them from the inside out, some, including these authors, refer to this organism as a pathogen of other bacteria and their is some discussion here and elsewhere for its potential to serve as a "living antibiotic" in much the same way people are trying to use bacterial viruses (a.k.a. phage).

The paper overall is quite nice on first read. They used microarray studies to characterize gene expression patterns in different phases of the life cycle (see Figure above for the life cycle outline). They backed up this work by quantitative PCR studies and regular RT PCR. And based upon their analysis they found some genes that are "Up-Regulated in Predatory, but Not HI" phase (HI stands for host-independent). And here is where they really tell us what they mean by predatosome:

This category of 240 genes are very interesting as they potentially exclude those genes simply involved with release from attack-phase into growth, namely they should be part of the “predatosome” of predatorily specific genes.

It seems to me this terminology is completely unnecessary. All they need to do is say they are studying the genes related to the predatory phase. To assign these genes to the "predatosome" is a bit much. They continue in the paper to report some really interesting stuff. For example, they also examine another predatory bacterial species, and look at whether there are genes conserved in the process between species. They made some really nice figures by the way about the different phases of hte life cycle in this organism and which genes are expressed:

Anyway - the science in the paper is nice. However, the invention of yet another omics word is a bit much. And thus Lambert et al. are winners of the highly coveted "Worst New Omics Word Award" for their invention of "predatosome". Details on the paper are below - and that is where the figures come from too. (Hat tip to Bora for letting me know about the paper, and the word).

Well, just a mini post here. In case you did not know - PLoS One is now being indexed by ISI (see their announcement: PLoS ONE and see the PLOS blog post here and see Erik Svensson's blog post for an interesting take) and will get an impact factor and be in their Citation Index and all such things. Now mind you, I think "Impact Factor" is a silly thing overall in that we should evaluate papers not journals per se.

So why am I writing this - because I find it pretty funny that despite being slow to recognize PLoS One ISI is now promoting the fact that they are indexing PLoS One on their home page. See the screen capture above.

Saturday, January 23, 2010

Robert Langreth in an article at Forbes.Com on January 20 (GlaxoSmithkline's Malaria Plan: Limit Profits, Open Labs) reports that Glaxo Smith Kline is becoming a bit more open with their data on malaria drug/vaccine development. Apparently, they plan to open up their labs and some of their data to non profit collaborators such as Emory University. Sounds like this could be a good first step. But if they really want to advance malaria vaccine research, perhaps they should release their data to everyone? I get that they want/need to make a profit, but if they want to try and get credit for being open, I think they really should jump into the deep end and do something radical. Just sharing bits and pieces of data with a few labs is not a particularly stunning move.

There were not an even number of males and females. Sure it was just a difference of one (133 men, 134 women). But come on that is so biased.

There were some sessions where some of the people attending the session were not live blogging or tweeting. I know, how could they? Well, it is possible their batteries ran out on their phones, but I mean, really, this is a meeting called "Science Online 2010". If you are going to go to such a meeting you must bring the right tools.

Someone bumped into the light switch during the keynote talk and shed light on it right when it was getting juicy. The atmosphere was crushed.

There have not yet been any books published about the meeting. It's true, in the sense that I did an Amazon search and did not find any (note to fact checkers - check that please).

The hotel had sleep number beds but did not provide any Youtube videos for how to use them. How are we expected to figure out what to do?

Nobody sequenced any genomes at the meeting. Yuck.

Some people took notes on paper. How on earth are they going to tweet while writing stuff down?

A new flu strain was created by all the recombining ideas and discussions of the sexual behaviors of ducks, cuttlefish and other organisms at the meeting. It is now known as scion flu, or H10N10. At least something form the meeting went viral.

Basically, the article is a detailed discussion of how examples relating to microbial eukaryotes (I hate the term protist ...) that are used by Intelligent Design advocates are, well, BS. And the article discusses the evidence that refutes the ID arguments.

One thing they discuss is the issue of the Cambrian Explosion. ID supporters, such as Stephen Meyer have made many arguments about they feel the diversification in the Cambrian is not explainable through evolutionary processes. Farmer and Habura refute this by pointing out that the diversity seen in microbial eukaryotes at the time of the Cambrian was immense and that what came out of the "explosion" was actually not that spectacular relative to what already existed in the microbial eukaryotes:

The extant diversity of the protists should therefore be seen as the "background radiation" of the eukaryotic Big Bang, with the Cambrian radiation of the metazoa being a subsequent event within a specific group.

They go on to discuss examples involving speciation, the fossil record, evolution of drug resistance in Plasmodium, and a few other things. In each case they discuss a claim by ID supporters and then discuss evidence for why this claim is not valid. Overall the paper is worth reading if you are involved in any discussions with ID supporters.

I note that when I finished the above writing, I went to look at Pubmed to find other examples of people taking on ID arguments in the literature with a focus on issues in microbes. Here are two other recent examples:

I am sitting in my hotel room, kind of wishing I had gotten an earlier flight back but also hoping that a friend of mine from NC State will have some free time tomorrow. Anyway- I will post more about the meeting later but wanted to put out a few things before I forget them here. Here is my List of the Top 11 things I learned or relearned at Science Online 2010.

Contrary to what some many claim, science journalism is not dead and I was really impressed by how much science reporters really care about the quality of their work

Systems like twitter, facebook, blogs, podcasts, slides, games are neither good nor bad but ALL can be used in good or bad ways in regard to communicating science (I kind of knew this already but have had it confirmed)

No matter how good sessions are at a meeting, the best stuff happens outside of sessions in the hall, bar, etc

Adding a bit of humor to a meeting or presentation is fantastic; and not done enough; in general, 'Science' needs more humor

Working hard to promote and market something you do is fine and in fact, very useful; but marketing something of little or no relevance (especially to a captive audience) - not so good

People with passion about their work (of which there were an amazing collection at the meeting) can get people interested in ANYTHING; people without passion, can suck the life out of the coolest thing ever

Though it is true that there are continuing issues with the existence of "anti-science" groups and movements, people still seem to inherently love science; related to this, a key task for science supporters is to focus attention on teaching critical thinking

Tuesday, January 12, 2010

I am posting this because I will be chairing a session this up coming weekend at Science Online 2010 on "Open Access" publishing.

And I would love input from everyone/anyone out there on what might be worth discussion at this session. Possible topics include

why open and free are not the same thing

open access mandates

financial aspects of OA

educational uses of OA literature

things that are slowing the inevitable spread of OA publishing

I am perhaps most interested these days in the last two on that list. For example - it seems that OA publishing would spread even faster if we did not have some very conservative styles of tenure, promotion, hiring and grant review processes.

If anyone has some pressing topics that you think are worth bringing up in a discussion of OA publishing, please post them here.

Monday, January 11, 2010

Just got this in my inbox - have never received any phishing directed at my gmail account before - maybe this is a follow up to google's issues with China?Gmail Alertreply-toinfotechcrewacess@gmail.com

to

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Just got this via Epernicus - is it a sign that Epernicus is attracted more attention? (For those who do not know, Epernicus is a professional networking system for scientists)

Nice To Meet You, How are you today ?,My name is (deleted) Hight,fair in completion ,i saw your profile today on (www.epernicus.com) and after going true it i was moved with the quality i found in your profile,which makes me to became interested in knowing you the more. but i will like you to no that distance ,age or color dose not matter but what maters is love and understanding and being honest to each other. i will like you contact me true my direct mailing address so that i will give you my picture and tell you more about me. (email deleted)i have SOMETHING VERY IMPORTANT to tell you.Good to hear from you, (email deleted) Yours dream love. And Happy New Year, (deleted)

Thursday, January 07, 2010

Just got this announcement for this important Fellowship program. A student who got her PhD in my lab just started in this program for this years group (see the SJ Mercury News Story about this program here). Love the flyer by the way "Can you apply the laws of science to the science of laws?". Email announcement is below:

"The California Council on Science and Technology (CCST) is pleased to announce that applications are now being accepted for the 2010-2011 California Science and Technology Policy Fellowships based in Sacramento.

The S&T Policy Fellowship, a unique one-year professional development opportunity, provides the selected fellows with hands-on experience working with the California Legislature to incorporate science and technology into public policy. Eligible applicants will be PhD-level (or equivalent) scientists and engineers who have a sincere interest in California current events, the state legislative process, and a strong desire to learn how policy decisions are made.

Please forward this announcement to any individuals or group listservs that may be interested in this exciting opportunity. Deadline for submission of applications is February 12, 2010 at 5:00 p.m. PST. More information is available at http://www.fellows.ccst.us."

Tuesday, January 05, 2010

A new paper just showed up on PLoS One and it has some serious potential to be important The paper (PLoS ONE: The Effects of Circumcision on the Penis Microbiome) reports on analyses that show differences in the microbiota (which they call the microbiome - basically what bacterial species were present) in men before and after circumcision. And they found some significant differences. It is a nice study of a relatively poorly examined subject - the bacteria found on the penis w/ and w/o circumcision. This is a particularly important topic in light of other studies that have shown that circumcision may provide some protection against HIV infection.

In summary here is what they did - take samples from men before and after circumcision. Isolate DNA. Run PCR amplification reactions to amplify variable regions of rRNA genes from these samples. Then conduct 454 sequencing of these amplified products. And then analyze the sequences to look at the types and #s of different kinds of bacteria.

What they found is basically summarized in their last paragraph

"This study is the first molecular assessment of the bacterial diversity in the male genital mucosa. The observed decrease in anaerobic bacteria after circumcision may be related to the elimination of anoxic microenvironments under the foreskin. Detection of these anaerobic genera in other human infectious and inflammatory pathologies suggests that they may mediate genital mucosal inflammation or co-infections in the uncircumcised state. Hence, the decrease in these anaerobic bacteria after circumcision may complement the loss of the foreskin inner mucosa to reduce the number of activated Langerhans cells near the genital mucosal surface and possibly the risk of HIV acquisition in circumcised men."

And this all sounds interesting and the work seems solid. I note that some friends / colleagues of mine were involved in this including Jacques Ravel who used to be at TIGR and now is at U MD and Paul Kiem who is associated with TGen in Arizona. For anyone interested in HIV, the human microbiome, circumcision, etc, it is probably worth looking at.

However, the press release I just saw from TGen really ticked me off. The title alone did me in "Study suggests why circumcised men are less likely to become infected with HIV". Sure the study did suggest a possible explanation for why circumcised men are less likely to get HIV infections - the paper was justifiably VERY cautious about this inference. They basically state that there are some correlations worth following up.

The press release goes on to say "The study ... could lead to new non-surgical HIV preventative strategies for the estimated 70 percent of men worldwide (more than 2 billion) who, because of religious or cultural beliefs, or logistic or financial barriers, are not likely to become circumcised." Well sure, I guess you could say that. I think they are iplying you could change the microbiome somehow and therefore protect from HIV but that implies (1) that there really is a causal relationship between the microbial differences in HIV protection and (2) that one could change the microbiome easily, which is a big big stretch given how little we know right now.

Anyway - the science seems fine and not over-reaching. But the press release is annoying and misleading. Shocking I know. But this one got to me.

This paper discusses "how changes in gene regulation and coding sequence contribute to sensory diversification in two replicate radiations of cichlid fishes." A good overview of the paper is in an accompanying article "Visual Tuning May Boost African Cichlid Diversity" by Robin Meadows:

"African cichlid fish form new species faster than any other vertebrates, with hundreds of species evolving within the last 2 million years in Lake Malawi and within the last 120,000 years in Lake Victoria. This rapid speciation makes cichlids good models for elucidating the genetic mechanisms behind biodiversity. Vision may play a key role in cichlid evolution, adapting them to forage for new foods or colonize new habitats. Vertebrate retinas have two groups of light-sensitive proteins called opsins: those in rod photoreceptors, which are sensitive to dim light, and those in cone photoreceptors, which are sensitive to color. Changes in the visual system could be due to differences either in the expression of opsin genes or in their DNA sequences. A Research Article in this issue of PLoS Biology by Christopher Hofmann and colleagues suggests that both mechanisms underlie changes in visual sensitivity in cichlids."

For more on the science, see her summary and see the article itself. Additional information can be found in the press release from U. MD

But what I wanted to cover here was some of the story behind the science. So I emailed the authors some questions which they were kind enough to answer and I post the details here. There are some really interesting tidbits in these answers in my opinion, including how they dealt with merging two papers into one, and how difficult (but fun) it is to do this field work in Lake Malawi.

In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University.

Among their findings:

"an invasive species of insect in a box of grapefruit from Texas"

"what could be a new species or subspecies of New York cockroach"

multiple mislabelled food products including (quoted from the press release, I note)

An expensive specialty “sheep’s milk” cheese made in fact from cow’s milk;

“Venison” dog treats made of beef;

“Sturgeon caviar” that was really Mississippi paddlefish;

A delicacy called “dried shark,” which proved to be freshwater Nile perch from Africa;

A label of “frozen yellow catfish” on walking catfish, an invasive species;

“Dried olidus” (smelt) that proved to be Japanese anchovy, an unrelated fish;

“Caribbean red snapper” that turned out to be Malabar blood snapper, a fish from Southeast Asia.

And what I find most interesting, is this built upon work of other students from Trinity Kate Stoeckle and Louisa Strauss who had done a restaurant based barcoding study last year.

This type of work is cool in so many ways. It gets students into science. It is an applied us of taxonomy (though I note, barcoding is not without controversy in the taxonomy community). It is a useful form of citizen science -- and may eventually provide a way to keep dishonest sellers on their toes ... Kudos to all involved in this